Load customized gene sets into work space. Pre-packaged genesets can also be used goslim.human.all goslim.human.BP goslim.human.CC goslim.human.MF goslim.mouse.all goslim.mouse.BP goslim.mouse.CC goslim.mouse.MF goslim.rat.all goslim.rat.BP goslim.rat.CC goslim.rat.MF goslim.yeast.all goslim.yeast.BP goslim.yeast.CC goslim.yeast.MF kegg2.5.generic
Print the results from geneListProfile(). The printing format can be MSigDB or 2 column (Gene_Set, number) format, where Gene_Set is the name of a gene set and number is the number of overlapping genes between the gene list and the gene set. In the MSigDB format the output contains all the overlapping gene symbols. The output can be stdin or directed to a file.
geneListPie package is for mapping a gene list to function categories defined in GOSlim or Kegg. The results can be plotted as a pie chart to provide a quick view of the genes distribution of the gene list among the function categories. The gene list must contain a list of gene symbols. The package contains a set of pre-processed gene sets obtained from Gene Ontology and MSigDB including human, mouse, rat and yeast. To provide a high level concise view, only GO slim and kegg are provided. The gene sets are regulared updated. User can also use customized gene sets. User can use the R Pie() or Pie3D() function for plotting the pie chart. Users can also choose to output the gene function mapping results and use external software such as Excel(R) for ploting.
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